A Comparison of Less Invasive SARS-CoV-2 Diagnostic Specimens in Nursing Home Residents — Arkansas, June–August 2020

Gable, Paige; Huang, Jennifer Y; Gilbert, Sarah E; Bollinger, Susan; Lyons, Amanda K; Sabour, Sarah; Surie, Diya; Biedron, Caitlin; Haney, Tafarra; Beshearse, Elizabeth; Gregory, Christopher J; Seely, Kathryn A; Clemmons, Nakia S; Patil, Naveen; Kothari, Atul; Gulley, Trent; Garner, Kelley; Anderson, Karen; Thornburg, Natalie J; Halpin, Alison L; McDonald, L Clifford; Kutty, Preeta K; Brown, Allison C

BACKGROUND: SARS-CoV-2 testing remains essential for early identification and clinical management of cases. We compared the diagnostic performance of three specimen types for characterizing SARS-CoV-2 in infected nursing home residents. METHODS: A convenience sample of 17 residents were enrolled within 15 days of first positive SARS-CoV-2 result by real-time reverse transcription polymerase chain reaction (RT-PCR) and prospectively followed for 42 days. Anterior nasal swabs (AN), oropharyngeal swabs (OP), and saliva specimens (SA) were collected on the day of enrollment, every 3 days for the first 21 days, then weekly for 21 days. Specimens were tested for presence of SARS-CoV-2 RNA using RT-PCR and replication-competent virus by viral culture. RESULTS: Comparing the three specimen types collected from each participant at each time point, the concordance of paired RT-PCR results ranged from 80–88%. After the first positive result, SA and OP were RT-PCR–positive for ≤48 days; AN were RT-PCR–positive for ≤33 days. AN had the highest percentage of RT-PCR–positive results (81%; 21/26) when collected ≤10 days of participants’ first positive result. Eleven specimens were positive by viral culture: nine AN collected ≤19 days following first positive result and two OP collected ≤5 days following first positive result. CONCLUSIONS: AN, OP, and SA were effective methods for repeated testing in this population. More AN than OP were positive by viral culture. SA and OP remained RT-PCR–positive longer than AN, which could lead to unnecessary interventions if RT-PCR detection occurred after viral shedding has likely ceased.